I've ended up having two new pilot bearings. One of them (SKF) has no play or wobble on the input shaft but still goes on easily, the other one (National) has some noticeable wobble but not what I'd call too loose. Which one should I use? I'm mainly concerned about which would have less chance of going bad over the long term.

 

since you have the 2, I would go with the one that fits best (less slop)

pilot bearing failure is mostly due to bad input shaft bearing or on install the tranny was pulled in using bolts because the clutch disc was not dead nuts aligned and the input shaft tip is hitting the edge of the bearing that gets killed when the tranny is forced in using the tranny bolts

otherwise the pilot bearing has a pretty passive function as it just supports the input shaft tip and should easily last 100k mi